Yoko was, in my opinion, criminally underused. As an excellent logical and emotional foil to Kamina and Simon, I was distressed to see her disappear from the show's main story for chunks of time.

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After Kamina dies, Yoko gets a bit of grieving time in a few episode, but is mostly overshadowed by Nia's arrival. Now, while I loved Nia, Yoko was a much more interesting and nuanced character. I wanted to see more of her post-Kamina's death, especially as a support to Simon.

Mostly, I felt like Yoko was pushed into a fanservice role (a true shame), rather than taking on the mentor role which would have been a perfect fit for her. She's capable, honest, and loyal, and to see her reduced to such a role was a bummer. As far as her checking out from the new government, I understand that, but the show basically ignored her until her return. That bummed me out.

In short, I loved her character and thought that she could have used much more screen time. I already love Gurren Lagann, and having more Yoko (as a character, not just a half-dressed piece of eye candy) would have made it even better.

To get to a proper pick.
Every Male-Best-Friend in EVERY Harem anime needs more screen time. Like seriously. Teen SNAFU introduced a rather manly looking best friend for our Lead, AND WE NEVER SEE HIM AFTER HIS INTRODUCTION. It's common as all hell, and it's stupid.
Makoto is just another one of those "Male best friend" characters.

Pretty much this for me, the guy who gets maybe like at most 2-3 mins of air time an episode (to sometimes season it seems) in Harems, they tend to be better than most of the other characters too.

I'd also say like every character in Fairy Tail that isn't a part of Team Natsu deserved more screen time than they got.

Since the show is named after her and all, It irritates me that they spent almost 1/3 of season one on everyone but her

That's.. oddly true! Index has the most passive role out of anybody and seems to be no more important to the series than the members of Anti-Skill.

If she stopped hanging around with Touma, she probably wouldn't get her own story..
She's a little nun girl from a supernatural mega church, has a photographic memory, knows the context of 103,000 forbidden books of magic, and the show is named after her.. and yet somehow Mr. Fist of Deus Ex Machina and his harem are deemed more important